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Detailed information for vg1007912566:

Variant ID: vg1007912566 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7912566
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGGCAAGCCGAGCAATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACAACTAAAA[T/C]
ATGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTC

Reverse complement sequence

GAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCAT[A/G]
TTTTAGTTGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACATTGCTCGGCTTGCCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 0.10% 0.25% 0.95% NA
All Indica  2759 99.30% 0.10% 0.43% 0.14% NA
All Japonica  1512 97.50% 0.00% 0.00% 2.51% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 0.30% 0.88% 0.11% NA
Indica Intermediate  786 99.20% 0.10% 0.25% 0.38% NA
Temperate Japonica  767 98.80% 0.00% 0.00% 1.17% NA
Tropical Japonica  504 95.20% 0.00% 0.00% 4.76% NA
Japonica Intermediate  241 97.90% 0.00% 0.00% 2.07% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 97.80% 0.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007912566 T -> C LOC_Os10g15100.1 intron_variant ; MODIFIER silent_mutation Average:24.853; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg1007912566 T -> DEL N N silent_mutation Average:24.853; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N